Pathways to dewetting in hydrophobic confinement

The surface tension of Martini 3 water mixtures

The Martini model, a coarse-grained forcefield for biomolecular simulations, has experienced a vast increase in popularity in the past decade. Its building-block approach balances computational efficiency with high chemical specificity, enabling the simulation of organic and inorganic molecules. The modeling of coarse-grained beads as Lennard-Jones particles poses challenges for the accurate reproduction of liquid-vapor interfacial properties, which are crucial in various applications, especially in the case of water. The latest version of the forcefield introduces refined interaction parameters for water beads, tackling the well-known artifact of Martini water freezing at room temperature. In addition, multiple sizes of water beads are available for simulating the solvation of small cavities, including the smallest pockets of proteins. This work focuses on studying the interfacial properties of Martini water, including surface tension and surface thickness. Employing the test-area method, we systematically compute the liquid-vapor surface tension across various combinations of water bead sizes and for temperatures from 300 to 350 K. These findings are of interest to the Martini community as they allow users to account for the low interfacial tension of Martini water by properly adjusting observables computed via coarse-grained simulations to allow for accurate matching against all-atom or experimental results. Surface tension data are also interpreted in terms of local enrichment of the various mixture components at the liquid-vapor interface by means of Gibbs' adsorption formalism. Finally, the critical scaling of the Martini surface tension with temperature is reported to be consistent with the critical exponent of the 3D Ising universality class.

Computational investigation of the effects of polymer grafting on the effective interaction between silica nanoparticles in water

Understanding and control of the effective interaction between nanoscale building blocks (colloids or nanoparticles) dispersed in a solvent is an important prerequisite for the development of bottom-up design strategies for soft functional materials. Here, we have employed all-atom molecular dynamics simulations to investigate the impact of polymer grafting on the solvent-mediated effective interaction between the silica nanoparticles (Si-NPs) in water, and in turn, on its bulk structural and thermodynamic properties. We found that the nature of the short grafting polymers [characterized by their interaction with water (hydrophobicity or hydrophilicity) and molecular weight] has a profound effect on the range and strength of the effective interaction between the Si-NPs. The hydrophobic polymer [such as polyethylene (PE)]-grafting of Si-NP gives rise to a more attractive interaction between the Si-NPs compared to the hydrophilic polymer [such as polyethylene glycol (PEG)] and non-grafted cases. This study further provides fundamental insights into the molecular origin of the observed behavior of the effective pair interactions between the grafted Si-NPs. For PE-grafted Si-NPs, the confined water (water inside the cavity formed by a pair of Si-NPs) undergoes a partial dewetting transition on approaching below a critical inter-particle separation leading to a stronger attractive interaction. Furthermore, we report that the effective attraction between the PE-grafted Si-NPs can be reliably controlled by changing the grafting PE density. We have also investigated the bulk structural and thermodynamic behavior of the coarse-grained Si-NP system where the particles interact via effective interaction in the absence of water. We believe that the insights gained from this work are important prerequisites for formulating rational bottom-up design strategies for functional materials where nano- (or, colloidal) particles are the building blocks.

On the engulfment of antifreeze proteins by ice

Antifreeze proteins (AFPs) are remarkable biomolecules that suppress ice formation at trace concentrations. To inhibit ice growth, AFPs must not only bind to ice crystals, but also resist engulfment by ice. The highest supercooling, [Formula: see text], for which AFPs are able to resist engulfment is widely believed to scale as the inverse of the separation, [Formula: see text], between bound AFPs, whereas its dependence on the molecular characteristics of the AFP remains poorly understood. By using specialized molecular simulations and interfacial thermodynamics, here, we show that in contrast with conventional wisdom, [Formula: see text] scales as [Formula: see text] and not as [Formula: see text]. We further show that [Formula: see text] is proportional to AFP size and that diverse naturally occurring AFPs are optimal at resisting engulfment by ice. By facilitating the development of AFP structure-function relationships, we hope that our findings will pave the way for the rational design of AFPs.

Preparation and investigation of two-component silica-modified hydrophobic layer for minimizing retention loss of reversed-phase chromatographic columns using fully aqueous mobile phases

Chromatographers often employ fully aqueous mobile phases to retain highly polar compounds in reversed-phase liquid chromatography (RPLC). However, when the flow rate is interrupted, either accidentally or intentionally, a substantial loss in retention occurs due to the spontaneous dewetting of water from the hydrophobic surface of conventional RPLC-C18 particles. Previous studies have shown that maintaining a low C18 surface coverage (approximately 1.5 μmol/m2) can mitigate water dewetting by increasing chain disorder, facilitating the intercalation of water clusters between the C18-bonded chains, and keeping the mesopores wetted. In this research, we explore the potential and additional benefits of using two-component surface bonding materials (C8/C18 and PhenylHexyl (PhHx)/C18) at a constant and low total surface coverage of 1.51 ± 0.15 μmol/m2. We synthesized seven one- and two-component modified silica particles with a volume average particle size of 5.22 μm and an average mesopore size of 104 Å. The surface coverage was increased from 0 to 0.54, 1.00, and to 1.66 μmol2 for C8 chains and from 0 to 0.52, 0.70, and to 1.65 μmol2 for PhHx ligands. To prevent interactions between water and any unreacted silanols, all seven derivatized particles were heavily endcapped with trimethylsilane (TMS) reagent. The fraction of the surface area remaining in contact with water was determined by measuring the retention times of weakly (thiourea) and strongly (thymine) retained compounds at intervals of 1, 2, 4, 8, 16, 32, and 64 minutes following the cessation of flow. Two distinct column temperatures, 24°C and 60°C, were employed in the experiments. Retention losses were found to be minimized in the presence of a small quantity of C8 chains (less than 40% of the total surface coverage). Additionally, it is essential to consider substantial fractions of PhHx chains, as long as the presence of the PhHx ligand does not significantly impact retention and selectivity. Combining mixed RPLC bondings with a low total surface coverage of approximately 1.5 μmol/m2 emerges as a viable solution for further minimizing retention loss in standard C18-bonded RPLC columns, particularly within the surface coverage range of 2.5-3.0 μmol/m2.

Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

In this work, we investigate the role of solvent in the binding reaction of the p53 transactivation domain (TAD) peptide to its receptor MDM2. Previously, our group generated 831 μs of explicit-solvent aggregate molecular simulation trajectory data for the MDM2-p53 peptide binding reaction using large-scale distributed computing and subsequently built a Markov State Model (MSM) of the binding reaction (Zhou et al. 2017). Here, we perform a tICA analysis and construct an MSM with similar hyperparameters while using only solvent-based structural features. We find a remarkably similar landscape but accelerated implied timescales for the slowest motions. The solvent shells contributing most to the first tICA eigenvector are those centered on Lys24 and Thr18 of the p53 TAD peptide in the range of 3-6 Å. Important solvent shells were visualized to reveal solvation and desolvation transitions along the peptide-protein binding trajectories. Our results provide a solvent-centric view of the hydrophobic effect in action for a realistic peptide-protein binding scenario.

What keeps nanopores boiling

The liquid-to-vapor transition can occur under unexpected conditions in nanopores, opening the door to fundamental questions and new technologies. The physics of boiling in confinement is progressively introduced, starting from classical nucleation theory, passing through nanoscale effects, and terminating with the material and external parameters that affect the boiling conditions. The relevance of boiling in specific nanoconfined systems is discussed, focusing on heterogeneous lyophobic systems, chromatographic columns, and ion channels. The current level of control of boiling in nanopores enabled by microporous materials such as metal organic frameworks and biological nanopores paves the way to thrilling theoretical challenges and to new technological opportunities in the fields of energy, neuromorphic computing, and sensing.

Classical nucleation of vapor between hydrophobic plates

In this work, an extended classical nucleation theory (CNT), including line tension, is used to disentangle classical and non-classical effects in the nucleation of vapor from a liquid confined between two hydrophobic plates at a nanometer distance. The proposed approach allowed us to gauge, from the available simulation work, the importance of elusive nanoscale effects, such as line tension and non-classical modifications of the nucleation mechanism. Surprisingly, the purely macroscopic theory is found to be in quantitative accord with the microscopic data, even for plate distances as small as 2 nm, whereas in extreme confinement ([Formula: see text] nm), the CNT approximations proved to be unsatisfactory. These results suggest how classical nucleation theory still offers a computationally inexpensive and predictive tool useful in all domains where nanoconfined evaporation occurs—including nanotechnology, surface science, and biology.

Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.

Stability of Water Confined between Supported Self-Assembled Monolayers

We present a thermodynamic argument showing that the evaporation and condensation free-energy barriers of water confined between two hydrophobic self-assembled monolayers (SAMs) vary more gradually with the SAM hydrophobicity as compared to the case of water confined between two bare hydrophobic surfaces (no SAMs). We validate our theory by calculating the free-energy profiles of water confined between two SAMs and between two bare surfaces of different hydrophobicities. An implication of our findings is the existence of three regimes of stability of confined water as a function of the hydrophobicity of the SAMs. In comparison to bare planar surfaces with no SAMs, the highly hydrophobic SAMs act to stabilize the liquid state, whereas weakly hydrophobic SAMs stabilize the vapor state of confined water. For intermediate hydrophobicities, the SAMs reduce both the evaporation and the condensation free-energy barriers. These results imply that the effects of SAM hydrophobicity on the behavior of confined water are nontrivial and richer than previously thought.

Solvent's Role in Cavity-Ligand Recognition Would Depend on the Mode of Ligand Diffusion

Solvent is known to play crucial roles in dictating the thermodynamics and kinetics of the biomolecular recognition process. Here, we show that the extent of significance of water in modulating the ligand recognition process is critically contingent on the ligand diffusion and on the constraints introduced on it. Toward the end, we use a well-known prototypical system of spherical ligand diffusing freely toward a hydrophobic concave cavity in explicit water. We analyze a large series of adaptively sampled unbiased molecular dynamics simulation trajectories within the framework of time-structured independent component analysis (TICA). Our quantitative investigations reveal that water would play a significant role in the ligand recognition process, provided that the ligand is constricted to diffuse along a centro-symmetric fashion. On the contrary, water's contribution in the ligand recognition process would diminish to a negligible value if the ligand freely diffuses toward the pocket. A Markov state model (MSM) constructed using the simulated trajectories identifies a set of transiently populated metastable states comprising partially ligand-unbound macro states, alongside ligand-bound and ligand-unbound pose and gives rise to multiple transition paths of ligand in its way to the hydrophobic cavity. Lifting the restriction on ligand movement changes its binding pathway, time scales, and the extent of the role of solvent in modulating the recognition process.

Subnanometer Topological Tuning of the Liquid Intrusion/Extrusion Characteristics of Hydrophobic Micropores

Intrusion (wetting)/extrusion (drying) of liquids in/from lyophobic nanoporous systems is key in many fields, including chromatography, nanofluidics, biology, and energy materials. Here we demonstrate that secondary topological features decorating main channels of porous systems dramatically affect the intrusion/extrusion cycle. These secondary features, allowing an unexpected bridging with liquid in the surrounding domains, stabilize the water stream intruding a micropore. This reduces the intrusion/extrusion barrier and the corresponding pressures without altering other properties of the system. Tuning the intrusion/extrusion pressures via subnanometric topological features represents a yet unexplored strategy for designing hydrophobic micropores. Though energy is not the only field of application, here we show that the proposed tuning approach may bring 20-75 MPa of intrusion/extrusion pressure increase, expanding the applicability of hydrophobic microporous materials.

Machine-Learned Free Energy Surfaces for Capillary Condensation and Evaporation in Mesopores

Using molecular simulations, we study the processes of capillary condensation and capillary evaporation in model mesopores. To determine the phase transition pathway, as well as the corresponding free energy profile, we carry out enhanced sampling molecular simulations using entropy as a reaction coordinate to map the onset of order during the condensation process and of disorder during the evaporation process. The structural analysis shows the role played by intermediate states, characterized by the onset of capillary liquid bridges and bubbles. We also analyze the dependence of the free energy barrier on the pore width. Furthermore, we propose a method to build a machine learning model for the prediction of the free energy surfaces underlying capillary phase transition processes in mesopores.

Structure and dynamics of water confined in cylindrical nanopores with varying hydrophobicity

We report a detailed study of the main structural and dynamical features of water confined in model Lennard-Jones nanopores with tunable hydrophobicity and finite length ([Formula: see text] Å). The generic model of cylindrical confinement used is able to reproduce the wetting features of a large class of technologically and biologically relevant systems spanning from crystalline nanoporous materials, to mesoporous silica and ion channels. The aim of this work is to discuss the influence of parameters such as wall hydrophobicity, temperature, and pore size on the structural and dynamical features of confined water. Our simulation campaign confirmed the existence of a core domain in which water displays bulk-like structural features even in extreme ([Formula: see text] Å) confinement, while dynamical properties were shown to depend non-trivially on the size and hydrophobicity of the pores. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Prediction of multiple dry-wet transition pathways with a mesoscale variational approach

Water fluctuates in a hydrophobic confinement, forming multiple dry and wet hydration states through evaporation and condensation. Transitions between such states are critical to both thermodynamics and kinetics of solute molecular processes, such as protein folding and protein-ligand binding and unbinding. To efficiently predict such dry-wet transition paths, we develop a hybrid approach that combines a variational implicit solvation model, a generalized string method for minimum free-energy paths, and the level-set numerical implementation. This approach is applied to three molecular systems: two hydrophobic plates, a carbon nanotube, and a synthetic host molecule Cucurbit[7]uril. Without an explicit description of individual water molecules, our mesoscale approach effectively captures multiple dry and wet hydration states, multiple dry-wet transition paths, such as those geometrically symmetric and asymmetric paths, and transition states, providing activation energy barriers between different states. Further analysis shows that energy barriers depend on mesoscopic lengths, such as the separation distance between the two plates and the cross section diameter of the nanotube, and that the electrostatic interactions strongly influence the dry-wet transitions. With the inclusion of solute atomic motion, general collective variables as reaction coordinates, and the finite-temperature string method, together with an improved treatment of continuum electrostatics, our approach can be further developed to sample an ensemble of transition paths, providing more accurate predictions of the transition kinetics.

Molecular Insights on the Wetting Behavior of a Surface Corrugated with Nanoscale Domed Pillars

Using all-atom molecular dynamics simulation, we investigated the wettability of a surface texturized with nanoscale pillars of domed, rectangular, or cylindrical shapes. The dewetted and wetted states of the gaps between the pillars were related to the Cassie-Baxter (CB) and Wenzel (WZ) states of a macroscopic water droplet resting on top of the pillars. We uncovered the structures and free energies of the intermediate states existing between the CB and WZ states. The contact line of the liquid-vapor-solid interface could not be depinned for the domed pillars due to their smooth curvatures unlike for the rectangular or cylindrical pillars. The liquid symmetrically penetrated down into the gap between the domed pillars by a liquid-vapor interface shape like a paraboloid, while the penetration for the rectangular or cylindrical pillars was often asymmetrical, giving a half-tubular liquid-vapor interface.

A molecular twist on hydrophobicity

A thorough exploration of the molecular basis for hydrophobicity with a comprehensive set of theoretical tools and an extensive set of organic solvent S/water binary systems is discussed in this work. Without a single exception, regardless of the nature or structure of S, all quantum descriptors of bonding yield stabilizing S⋯water interactions, therefore, there is no evidence of repulsion and thus no reason for etymological hydrophobicity at the molecular level. Our results provide molecular insight behind the exclusion of S molecules by water, customarily invoked to explain phase separation and the formation of interfaces, in favor of a complex interplay between entropic, enthalpic, and dynamic factors. S⋯water interfaces are not just thin films separating the two phases; instead, they are non-isotropic regions with density gradients for each component whose macroscopic stability is provided by a large number of very weak dihydrogen contacts. We offer a definition of interface as the region in which the density of the components in the A/B binary system is not constant. At a fundamental level, our results contribute to better current understanding of hydrophobicity.

Notwithstanding the very weak nature of individual contacts, it is the cumulative effect of a large number of interactions (green NCI surfaces) which provides macroscopic stability to the interfaces.

Understanding Design Rules for Optimizing the Interface between Immobilized Enzymes and Random Copolymer Brushes

A long-standing goal in the field of biotechnology is to develop and understand design rules for the stabilization of enzymes upon immobilization to materials. While immobilization has sometimes been successful as a strategy to stabilize enzymes, the design of synthetic materials that stabilize enzymes remains largely empirical. We sought to overcome this challenge by investigating the mechanistic basis for the stabilization of immobilized lipases on random copolymer brush surfaces comprised of poly(ethylene glycol) methacrylate (PEGMA) and sulfobetaine methacrylate (SBMA), which represent novel heterogeneous supports for immobilized enzymes. Using several related but structurally diverse lipases, including Bacillus subtilis lipase A (LipA), Rhizomucor miehei lipase, Candida rugosa lipase, and Candida antarctica lipase B (CALB), we showed that the stability of each lipase at elevated temperatures was strongly dependent on the fraction of PEGMA in the brush layer. This dependence was explained by developing and applying a new algorithm to quantify protein surface hydrophobicity, which involved using unsupervised cluster analysis to identify clusters of hydrophobic atoms. Characterization of the lipases showed that the optimal brush composition correlated with the free energy of solvation per enzyme surface area, which ranged from -17.1 kJ/mol·nm² for LipA to -11.8 kJ/mol·nm² for CALB. Additionally, using this algorithm, we found that hydrophobic patches consisting of aliphatic residues had a higher free energy than patches consisting of aromatic residues. By providing the basis for rationally tuning the interface between enzymes and materials, this understanding will transform the use of materials to reliably ruggedize enzymes under extreme conditions.

Characterizing the Interplay between Polymer Solvation and Conformation

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.

Intercalation-deintercalation of water-in-salt electrolytes in nanoscale hydrophobic confinement

Intercalation-deintercalation of water-in-salt (WIS) electrolytes in nanoscale confinement is an important phenomenon relevant to energy storage and self-assembly applications. In this article, we use molecular simulations to investigate the effects of intersurface separation on the structure and free energy underlying the intercalation-deintercalation of the Li bis(trifluoromethane)sulfonimide ([Li][TFSI]) water-in-salt (WIS) electrolyte confined between nanoscale hydrophobic surfaces. We employ enhanced sampling to estimate the free energy profiles for the intercalation behaviour of WIS in confining sheets at several intersurface separations. We observe that the relative stability of the condensed and vapour phases of WIS in the confinement depends on the separation between the confining surfaces and the WIS concentration. We find that the critical separation at which the condensed and vapour phases are equally stable in confinement depends on the concentration of WIS. The relative height of the free energy barrier also strongly depends on the concentration of [Li][TFSI] inside the confined space, and we find that this concentration dependence can be attributed to changes in line tension. The process of deintercalation passes through vapour tube formation inside the confined space, and this process is initiated by vapour bubble formation. The size of the critical vapour tube required for spontaneous evaporation of WIS from the confinement is also found to depend on the intersurface separation and WIS concentration.

Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint

The free energy of pore formation in lipid bilayers has been previously calculated using a variety of reaction coordinates. Here, we use free energy perturbation of a cylindrical lipid exclusion restraint to compute the free energy profile as a function of pore radius in dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) bilayers. Additionally restraining the headgroups to lie on the membrane surface allows us to also calculate the free energy profile of hydrophobic pores, i.e., cylindrical pores lined by acyl chains. For certain pore radii, the free energy of wetting of hydrophobic pores is calculated using the density bias method. It is found that wetting of hydrophobic pores becomes thermodynamically favorable at 5.0 Å for DMPC and 6.5 Å for DOPC, although significant barriers prevent spontaneous wetting of the latter on a nanosecond time scale. The free energy of transformation of hydrophilic pores to hydrophobic ones is also calculated using free energy perturbation of headgroup restraints along the bilayer normal. This quantity, along with wetting and pore growth free energies, provides complete free energy profiles as a function of radius. Pore line tension values for the hydrophilic pores obtained from the slope of the free energy profiles are 37.6 pN for DMPC and 53.7 pN for DOPC. The free energy profiles for the hydrophobic pores are analyzed in terms of elementary interfacial tensions. It is found that a positive three-phase line tension is required to explain the results. The estimated value for this three-phase line tension (51.2 pN) lies within the expected range.

Retention Loss of Reversed-Phase Columns Using Highly Aqueous Mobile Phases: Fundamentals, Mechanism, and Practical Solutions

We investigate a phenomenon observed by many practitioners of reversed- phase LC: a dramatic loss in retention volume or time after the column flow is stopped and resumed when using highly aqueous mobile phases with certain columns.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Pressure Induced Wetting and Dewetting of the Nonpolar Pocket of Deep-Cavity Cavitands in Water

Hydrophobic interactions drive the binding of nonpolar ligands to the oily pockets of proteins and supramolecular species in aqueous solution. As such, the wetting of host pockets is expected to play a critical role in determining the thermodynamics of guest binding. Here we use molecular simulations to examine the impact of pressure on the wetting and dewetting of the nonpolar pockets of a series of deep-cavity cavitands in water. The portals to the cavitand pockets are functionalized with both nonpolar (methyl) and polar (hydroxyl) groups oriented pointing either upward or inward toward the pocket. We find wetting of the pocket is favored by the hydroxyl groups and dewetting is favored by the methyl groups. The distribution of waters in the pocket is found to exhibit a two-state-like equilibrium between wet and dry states with a free energy barrier between the two states. Moreover, we demonstrate that the pocket hydration of the cavitands can be collapsed onto a unified adsorption isotherm by assuming the effective pressures within each cavitand pocket differ by a shift pressure that depends on the chemical identity and number of functional groups placed about the portal. These observations support the development of a two-state capillary evaporation model that accurately describes the equilibrium between states and naturally gives rise to the effective shift pressures observed from simulation. This work demonstrates that the hydration of host pockets can be tuned following simple design rules that in turn are expected to impact the thermodynamics of guest complexation.

Probing the concept of line tension down to the nanoscale

A novel mechanical approach is developed to explore by means of atom-scale simulation the concept of line tension at a solid-liquid-vapor contact line as well as its dependence on temperature, confinement, and solid/fluid interactions. More precisely, by estimating the stresses exerted along and normal to a straight contact line formed within a partially wet pore, the line tension can be estimated while avoiding the pitfalls inherent to the geometrical scaling methodology based on hemispherical drops. The line tension for Lennard-Jones fluids is found to follow a generic behavior with temperature and chemical potential effects that are all included in a simple contact angle parameterization. Former discrepancies between theoretical modeling and molecular simulation are resolved, and the line tension concept is shown to be robust down to molecular confinements. The same qualitative behavior is observed for water, but the line tension at the wetting transition diverges or converges toward a finite value depending on the range of solid/fluid interactions at play.

Dynamical control by water at a molecular level in protein dimer association and dissociation

Water, often termed as the "lubricant of life," is expected to play an active role in navigating protein dissociation-association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1-2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance R_MM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50-60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the "hotspot" region.

A unified description of hydrophilic and superhydrophobic surfaces in terms of the wetting and drying transitions of liquids

Clarifying the factors that control the contact angle of a liquid on a solid substrate is a long-standing scientific problem pertinent across physics, chemistry, and materials science. Progress has been hampered by the lack of a comprehensive and unified understanding of the physics of wetting and drying phase transitions. Using various theoretical and simulational techniques applied to realistic fluid models, we elucidate how the character of these transitions depends sensitively on both the range of fluid-fluid and substrate-fluid interactions and the temperature. Our calculations uncover previously unrecognized classes of surface phase diagram which differ from that established for simple lattice models and often assumed to be universal. The differences relate both to the topology of the phase diagram and to the nature of the transitions, with a remarkable feature being a difference between drying and wetting transitions which persists even in the approach to the bulk critical point. Most experimental and simulational studies of liquids at a substrate belong to one of these previously unrecognized classes. We predict that while there appears to be nothing particularly special about water with regard to its wetting and drying behavior, superhydrophobic behavior should be more readily observable in experiments conducted at high temperatures than at room temperature.

Nucleation of Capillary Bridges and Bubbles in Nanoconfined CO2

Using molecular simulation, we examine the capillary condensation and the capillary evaporation of CO₂ in cylindrical nanopores. More specifically, we employ the recently developed μV T-S method to determine the microscopic mechanism associated with these processes and the corresponding free energy profiles. We calculate the free energy barrier for capillary condensation and identify that the key step consists in the nucleation of a liquid bridge of a critical size. Similarly, the free energy maximum found for the capillary evaporation process is found to correspond to the nucleation of a vapor bubble of a critical size. In addition, we assess the impact of the strength of the wall-fluid on the height of the free energy barrier and on the critical size of liquid bridges (condensation process) and vapor bubbles (evaporation process). We observe that the height of the free energy barrier increases with the strength of the wall-fluid interactions. Finally, we build a theoretical model, based on capillary theory, to rationalize our findings. In particular, the simulation results reveal a linear scaling of the free energy barrier with the critical size, in excellent agreement with the theoretical predictions.

Retention loss of reversed-phase chromatographic columns using 100% aqueous mobile phases from fundamental insights to best practice

This work deals with experimental investigations pertaining to the impact of chemical (electrolyte concentration from 0 to 100 mM, dissolved nitrogen gas from 0 to 6.7  ×  10^-4 M in water; surface chemistry including hexylphenyl, polyphenyl, C₃₀, C₁₈, and C₈; surface coverage in C₁₈-bonded chains from 1.5 to 3.5 µmol/m²; presence of surface dopant), physical (hydrostatic pressure of water from 50 to 500 bar; temperature from 27 ^∘C to 75 ^∘C), and structural parameters (average pore size from 50 Å to 400 Å; pore connectivity) on the dewetting kinetics of water from the hydrophobic mesopores of particles packed in RPLC columns. The results are explained from physico-chemical viewpoints involving intrusion and extrusion Laplace pressures, advancing and receding contact angles, surface tension of water, vapor pressure of water, 3D reconstruction of the actual mesoporous structure, pore connectivity, and the hysteresis in nitrogen adsorption and desorption isotherm onto reversed-phase chromatographic materials. A model of water dewetting consistent with the observations and the physical interpretations is then proposed. Finally, the most relevant practical solutions (pressurizing the column in absence of flow, pore size enlargement, using phenyl-bonded phase, polar embedded or surface doped C₁₈-bonded phases, reducing the C₁₈ surface coverage, doping the silica surface, lengthening of the alkyl-bonded chains, applying low temperatures, purging and degassing the mobile phase with helium gas) are suggested in order to eliminate or at least minimize the retention loss of RPLC columns when using fully aqueous mobile phases.

Anomalous Stability of Two-Dimensional Ice Confined in Hydrophobic Nanopores

The freezing of water mostly proceeds via heterogeneous ice nucleation, a process in which an effective nucleation medium not only expedites ice crystallization but also may effectively direct the polymorph selection of ice. Here, we show that water confined within a hydrophobic slit nanopore exhibits a freezing behavior strongly distinguished from its bulk counterpart. Such a difference is reflected by a strong, non-monotonic pore-size dependence of freezing temperature but, more surprisingly, by an unexpected stacking ordering of crystallized two-dimensional ice containing just a few ice layers. In particular, confined trilayer ice is found to exclusively crystallize into a well-ordered, hexagonal stacking sequence despite the fact that nanopore exerts no explicit constraint on stacking order. The absence of cubic stacking sequence is found to be originated from the intrinsically lower thermodynamic stability of cubic ice over hexagonal ice at the interface, which contrasts sharply the nearly degenerated stability of bulk hexagonal and cubic ices. Detailed examination clearly reveals that the divergence is attributed to the inherent difference between the two ice polymorphs in their surface phonon modes, which is further found to generically occur at both hydrophobic and hydrophilic surfaces.

Pore Morphology Determines Spontaneous Liquid Extrusion from Nanopores

In this contribution we explore by means of experiments, theory, and molecular dynamics the effect of pore morphology on the spontaneous extrusion of nonwetting liquids from nanopores. Understanding and controlling this phenomenon is central for manipulating nanoconfined liquids, e. g., in nanofluidic applications, drug delivery, and oil extraction. Qualitatively different extrusion behaviors were observed in high-pressure water intrusion-extrusion experiments on porous materials with similar nominal diameter and hydrophobicity: macroscopic capillary models and molecular dynamics simulations revealed that the very presence or absence of extrusion is connected to the internal morphology of the pores and, in particular, to the presence of small-scale roughness or pore interconnections. Additional experiments with mercury confirmed that this mechanism is generic for nonwetting liquids and is rooted in the pore topology. The present results suggest a rational way to engineer heterogeneous systems for energy and nanofluidic applications in which the extrusion behavior can be controlled via the pore morphology.

Kinetic mechanism of water dewetting from hydrophobic stationary phases utilized in liquid chromatography

An experimental protocol was designed to accurately measure the dewetting kinetics of aqueous mobile phases from reversed-phase liquid chromatography (RPLC) columns. The protocol enables the determination of the losses in the wetted surface area and internal pore volume (leading to undesirable retention losses) of RPLC columns as a function of the dewetting time. It is used to evaluate the impact of the buffer/salt concentration in water (0-100 mM), nitrogen concentration dissolved in water (0-6.7 × 10^-4 M), column temperature (300-358 K), and of the internal structure (pore connectivity) of the stationary phase on the dewetting kinetics of various RPLC packing materials. From a fundamental viewpoint, the experimental facts demonstrate that dewetting kinetics are not solely driven by the pore size of the stationary phase and the contact angle with water. Temperature has a major influence on dewetting kinetics as it controls the nucleation rate of isolated water vapor bubbles over the entire mesoporous network. Additionally, the internal microstructure of the stationary phase (characterized by its internal porosity, pore size distribution, and pore connectivity) influences the rate at which the water vapor bubbles grow and coalesce in the entire particle volume. From a more practical viewpoint, the retention loss of RPLC columns due to water dewetting can be eliminated or at least minimized by (1) adjusting the surface and bonding chemistries to reduce the receding contact angle, (2) elevating the column outlet pressure, (3) operating at the lowest possible temperature, (4) minimizing the pore connectivity of the stationary phase (e.g., by increasing the degree of surface functionalization from C₈ to C₁₈-bonded phases), and (5) by degassing the aqueous mobile phase from any dissolved gases.

Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes

Hydrophobic effects drive diverse aqueous assemblies, such as micelle formation or protein folding, wherein the solvent plays an important role. Consequently, characterizing the free energetics of solvent density fluctuations can lead to important insights into these processes. Although techniques such as the indirect umbrella sampling (INDUS) method can be used to characterize solvent fluctuations in static observation volumes of various sizes and shapes, characterizing how the solvent mediates inherently dynamic processes, such as self-assembly or conformational change, remains a challenge. In this work, we generalize the INDUS method to facilitate the enhanced sampling of solvent fluctuations in dynamical observation volumes, whose positions and shapes can evolve. We illustrate the usefulness of this generalization by characterizing water density fluctuations in dynamical volumes pertaining to the hydration of flexible solutes, the assembly of small hydrophobes, and conformational transitions in a model peptide. We also use the method to probe the dynamics of hard spheres.

Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers

Understanding how material properties affect hydrophobic interactions-the water-mediated interactions that drive the association of nonpolar materials-is vital to the design of materials in contact with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM-SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.

Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes

We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r _n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r _n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.

Thermodynamically driven assemblies and liquid-liquid phase separations in biology

The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.

Characterizing surface wetting and interfacial properties using enhanced sampling (SWIPES)

We introduce an accurate and efficient method for characterizing surface wetting and interfacial properties, such as the contact angle made by a liquid droplet on a solid surface, and the vapor-liquid surface tension of a fluid. The method makes use of molecular simulations in conjunction with the indirect umbrella sampling technique to systematically wet the surface and estimate the corresponding free energy. To illustrate the method, we study the wetting of a family of Lennard-Jones surfaces by water. For surfaces with a wide range of attractions for water, we estimate contact angles using our method, and compare them with contact angles obtained using droplet shapes. Notably, our method is able to capture the transition from partial to complete wetting as surface-water attractions are increased. Moreover, the method is straightforward to implement and is computationally efficient, providing accurate contact angle estimates in roughly 5 nanoseconds of simulation time.

Quantitative Assessment of Thermodynamic Theory in Elucidating the Behavior of Water under Hydrophobic Confinement

A macroscopic thermodynamics-based theory that can quantitatively describe the behavior of water confined between hydrophobic solutes has so far remained elusive. In this work, we progress toward this goal by comparing the predictions of macroscopic theory with the results from computer simulations. We have determined free energy profiles of water confined between two nanometer-sized surfaces of varying hydrophobicity using molecular simulations and have estimated thermodynamic properties such as contact angle, line tension, and size of the critical vapor tube from independent simulations. We show that the scaling of free energy barrier to evaporation is fairly well captured by the factor ( D/2 + λ/ϒ_LV)², where D is the confinement gap and λ/ ϒ_LV is the ratio of line-tension and liquid-vapor surface tension. The radius of the critical vapor tube necessary for nucleating evaporation scales by the factor ( D/2 + λ/ϒ_LV). Exclusion of the line-tension term from thermodynamic theory leads to a qualitative disagreement between theoretical predictions and results from molecular simulations. We also demonstrate that macroscopic theory that includes the line-tension term is able to quantitatively match the entire free energy profile associated with the formation of a vapor-tube inside the confined region for conditions when the vapor state is the most stable state. The match is however only qualitatively correct for the conditions when the liquid state is more stable. Overall, the conclusion is that the inclusion of line-tension in macroscopic theory is necessary to describe the behavior of water under nanoscale confinement between two hydrophobic solutes.

Solvent-mediated interactions between nanostructures: From water to Lennard-Jones liquid

Solvent-mediated interactions emerge from complex mechanisms that depend on the solute structure, its wetting properties, and the nature of the liquid. While numerous studies have focused on the first two influences, here, we compare the results from water and Lennard-Jones liquid in order to reveal to what extent solvent-mediated interactions are universal with respect to the nature of the liquid. Besides the influence of the liquid, the results were obtained with classical density functional theory and brute-force molecular dynamics simulations which allow us to contrast these two numerical techniques.

Temperature Effects on Water-Mediated Interactions at the Nanoscale

We perform molecular dynamics simulations to study the effects of temperature on the water-mediated interactions between nanoscale apolar solutes. Specifically, we calculate the potential of mean force (PMF) between two graphene plates immersed in water at 240 ≤ T ≤ 400 K and P = 0.1 MPa. These are thermodynamic conditions relevant to cooling- and heating-induced protein denaturation. It is found that both cooling and heating tend to suppress the attraction, and ultimate collapse, of the graphene plates. However, the underlying role played by water upon heating and cooling is different. Isobaric heating reduces the strength and range of the interactions between the plates. Instead, isobaric cooling stabilizes the plates separations that can accommodate an integer number of water layers between the graphene plates. In particular, the energy barriers separating these plate separations increase linearly with 1/ T. We also explore the sensitivity of the plates PMF to the water model employed. In the case of the TIP4P/2005 model, water confined between the plates crystallizes into a defective bilayer ice at low temperatures, whereas in the case of the SPC/E model, water remains in the liquid state at same thermodynamic conditions. The effects of varying water-graphene interactions on the plates PMF are also studied.

Ice-Liquid Oscillations in Nanoconfined Water

Nanoscale confinement has a strong effect on the phase behavior of water. Studies in the last two decades have revealed a wealth of novel crystalline and quasicrystalline structures for water confined in nanoslits. Less is known, however, about the nature of ice-liquid coexistence in extremely nanoconfined systems. Here, we use molecular simulations to investigate the ice-liquid equilibrium for water confined between two nanoscopic disks. We find that the nature of ice-liquid phase coexistence in nanoconfined water is different from coexistence in both bulk water and extended nanoslits. In highly nanoconfined systems, liquid water and ice do not coexist in space because the two-phase states are unstable. The confined ice and liquid phases coexist in time, through oscillations between all-liquid and all-crystalline states. The avoidance of spatial coexistence of ice and liquid originates on the non-negligible cost of the interface between confined ice and liquid in a small system. It is the result of the small number of water molecules between the plates and has no analogue in bulk water.

Study of distance dependence of hydrophobic force between two graphene-like walls and a signature of pressure induced structure formation in the confined water

We examine the separation distance dependence of the hydrophobic force by systematically varying the distance (d) between two walls. The hydrophobic force exhibits a distance mediated crossover from a liquid-like to a gas-like behavior at around d ∼ 12 Å for 1 atm pressure. The distance dependence can be fitted to a bi-exponential form, with the longer distance part displaying a correlation length of 20 Å. In addition, the crossover is found to be accompanied by a divergent-like growth of the local relative number fluctuation of the water molecules confined between the two surfaces. Furthermore, at a fixed separation (d = 20 Å), we observe a pressure induced structural modification of confined water at high pressure. The confined water is found to form an ordered structure at high pressure (10 000 atm) and room temperature, in agreement with the experimental study [G. Algara-Siller et al. Nature 519(7544), 443 (2015)].

Communication: Relationship between local structure and the stability of water in hydrophobic confinement

Liquid water confined between nanoscale hydrophobic objects can become metastable with respect to its vapor at nanoscale separations. While the separations are only several molecular diameters, macroscopic theories are often invoked to interpret the thermodynamics and kinetics of water under confinement. We perform detailed rate and free energy calculations via molecular simulations in order to assess the dependence of the rate of evaporation, free energy barriers, and free energy differences between confined liquid and vapor upon object separation and compare them to the relevant macroscopic theories. At small enough separations, the rate of evaporation appears to deviate significantly from the predictions of classical nucleation theory, and we attribute such deviations to changes in the structure of the confined liquid film. However, the free energy difference between the confined liquid and vapor phases agrees quantitatively with macroscopic theory, and the free energy barrier to condensation displays qualitative agreement. Overall, the present work suggests that theories attempting to capture the kinetic behavior of nanoscale systems should incorporate structural details rather than treating it as a continuum.

Alchemical free energy calculations and umbrella sampling with local molecular field theory

Understanding the thermodynamic driving forces underlying any chemical process requires a description of the underlying free energy surface. However, computation of free energies is difficult, often requiring advanced sampling techniques. Moreover, these computations can be further complicated by the evaluation of any long-ranged interactions in the system of interest, such as Coulomb interactions in charged and polar media. Local molecular field theory is a promising approach to avoid many of the conceptual and computational difficulties associated with long-ranged interactions. We present frameworks for performing alchemical free energy calculations and non-Boltzmann sampling with local molecular field theory. We demonstrate that local molecular field theory can be used to perform these free energy calculations with accuracy comparable to traditional methodologies while eliminating the need for explicit treatment of long-ranged interactions in simulations.